Hi,
the TQMa6x starter kit used this approach, but I think they corrected it in the following revision and are now using another PHY.
I saw some workaround patches for said starter kit, which forced auto-negotiation master mode, but this was not a satisfying solution for us.
I think ENET_REF_CLK drives RGMII_TXC directly.
I strongly recommend using a separate 125 MHz oscillator with good (25ppm) frequency stability, I don't think you are saving much by using CLK125_NDO as ENET_REF_CLK.
Also, the ENET_REF_CLK does not have to be "in sync" with the PHYs 25 MHz clock, therefore a separate oscillator is the best solution.
In the end we decided to use a Marvell 88E1510 PHY (which is working great btw.) and although that PHY also has a 125 MHz clock output, it is not supported to use as reference clock for the MAC as it is only used for PTP etc. They explicitly tell you in the datasheet that it's not supported to use as MAC reference clock.
Maybe Micrel planned to give customers a cheap alternative to an external oscillator, but according to mentioned errata, it did not work out.
We use an oscillator from Abracon, the ASEMPC-125.000MHZ-LR-T as ENET_REF_CLK input. For more information see http://www.abracon.com/Oscillators/ASEMP.pdf